The $1.4 billion Ballpark Village project sustained a stunning reversal last night.

The community planning organization that advises the San Diego City Council on downtown redevelopment asked the council to kill altogether – not revise – the 3.2-million-square-foot office, residential and retail project, the city's largest and costliest.

The organization, the Centre City Advisory Committee, voted in May to support different provisions of a deal for the Ballpark Village master plan.

After nearly two years of planning and numerous appearances before the planning organization, JMI Realty, the development arm of Padres owner John Moores, and its partner, Lennar-San Diego Urban Division, announced details Sept. 20 of a secret deal negotiated over six weeks with a coalition of labor, environmental and housing groups.

The new deal would undo one negotiated with the Centre City Development Corp. board, which carries out downtown planning for the council.

The CCDC deal required JMI and Lennar to fully pay to build 82 affordable-housing condominiums with restricted prices within the six-block project area across Park Boulevard from Petco Park.

The new deal would scrap the condominiums and build low-income rental housing elsewhere. JMI and Lennar would pay Father Joe Carroll, president of St. Vincent de Paul homeless programs, about $17 million to redevelop three sites St. Vincent de Paul owns in East Village with 209 rental studios and apartments.

The financing for Carroll's deal is $17 million short, and San Diego city affordable housing funds might be tapped to fill that gap, said Pam Hamilton, a CCDC vice president.

One of the St. Vincent de Paul sites, which would have an 88-unit, nine-story family apartment building, straddles an earthquake fault, and the other sites are encumbered by older, complex deals negotiated for the public, Hamilton said.

The secret negotiations went "around the process to get affordable housing," and the new deal left too many questions unanswered, said Jennifer Ayala, an East Village representative on the Centre City Advisory Committee.

Bill Keller, who represents the Gaslamp Quarter, voted with the minority against rejecting the substitute deal, saying downtown was losing too much rental housing.

Advisory committee member Charles Hansen said he was more used to the "glacial glide" of public deals and "puzzled" over why JMI and the coalition were in such a rush to get the committee to adopt the new plan before consideration by the City Council on Oct. 11.

The deal with the coalition, which expires Oct. 18, also would require JMI and Lennar to pay $10-per-hour minimum wages, provide job training and meet other obligations.

The advisory group could have taken various actions last night, such as rejecting the new deal and reaffirming the old one. Instead, it recommended that the City Council "vote down the entire project due to lack of funding and changes" to the deal.

The group "also wants to remind the community to follow the proper process," it said.

The City Council, which is the Redevelopment Agency, has the final say on Ballpark Village.